101
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Bárdfalvy D, Nordanger H, Nardini C, Morozov A, Stenhammar J. Particle-resolved lattice Boltzmann simulations of 3-dimensional active turbulence. SOFT MATTER 2019; 15:7747-7756. [PMID: 31393504 DOI: 10.1039/c9sm00774a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Collective behaviour in suspensions of microswimmers is often dominated by the impact of long-ranged hydrodynamic interactions. These phenomena include active turbulence, where suspensions of pusher bacteria at sufficient densities exhibit large-scale, chaotic flows. To study this collective phenomenon, we use large-scale (up to N = 3 × 106) particle-resolved lattice Boltzmann simulations of model microswimmers described by extended stresslets. Such system sizes enable us to obtain quantitative information about both the transition to active turbulence and characteristic features of the turbulent state itself. In the dilute limit, we test analytical predictions for a number of static and dynamic properties against our simulation results. For higher swimmer densities, where swimmer-swimmer interactions become significant, we numerically show that the length- and timescales of the turbulent flows increase steeply near the predicted finite-system transition density.
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Affiliation(s)
- Dóra Bárdfalvy
- Division of Physical Chemistry, Lund University, Box 124, S-221 00 Lund, Sweden.
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102
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Anand SK, Chelakkot R, Singh SP. Beating to rotational transition of a clamped active ribbon-like filament. SOFT MATTER 2019; 15:7926-7933. [PMID: 31538995 DOI: 10.1039/c9sm01386e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a detailed study of a clamped ribbon-like filament under a compressive active force using Brownian dynamics simulations. We show that a clamped ribbon-like filament is able to capture beating as well as rotational motion under the compressive force. The nature of oscillation is governed by the torsional rigidity of the filament. The frequency of oscillation is almost independent of the torsional rigidity. The beating of the filament gives a butterfly-shaped trajectory of the free-end monomer, whereas rotational motion yields a circular trajectory on a plane. The binormal correlation and the principal component analysis reveal the butterfly, elliptical, and circular trajectories of the free end monomer. We present a phase diagram for different kinds of motion in the parameter regime of compressive force and torsional rigidity.
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Affiliation(s)
- Shalabh K Anand
- Department of Physics, Indian Institute of Science Education and Research, Bhopal 462 066, Madhya Pradesh, India.
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103
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Porter MK, Preska Steinberg A, Ismagilov RF. Interplay of motility and polymer-driven depletion forces in the initial stages of bacterial aggregation. SOFT MATTER 2019; 15:7071-7079. [PMID: 31441486 DOI: 10.1039/c9sm00791a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Motile bacteria are often found in complex, polymer-rich environments in which microbes can aggregate via polymer-induced depletion forces. Bacterial aggregation has many biological implications; it can promote biofilm formation, upregulate virulence factors, and lead to quorum sensing. The steady state aggregation behavior of motile bacteria in polymer solutions has been well studied and shows that stronger depletion forces are required to aggregate motile bacteria as compared with their nonmotile analogs. However, no one has studied whether these same trends hold at the initial stages of aggregation. We use experiments and numerical calculations to investigate the polymer-induced depletion aggregation of motile Escherichia coli in polyethylene glycol solutions on short experimental timescales (∼10 min). Our work reveals that in the semi-dilute polymer concentration regime and at short timescales, in contrast to what is found at steady state, bacterial motility actually enhances aggregate formation by increasing the collision rate in viscous environments. These unexpected findings have implications for developing models of active matter, and for understanding bacterial aggregation in dynamic, biological environments, where the system may never reach steady state.
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Affiliation(s)
- Michael K Porter
- Division of Chemistry & Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA.
| | - Asher Preska Steinberg
- Division of Chemistry & Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA.
| | - Rustem F Ismagilov
- Division of Chemistry & Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA. and Division of Biology & Biological Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
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104
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Koumakis N, Brown AT, Arlt J, Griffiths SE, Martinez VA, Poon WCK. Dynamic optical rectification and delivery of active particles. SOFT MATTER 2019; 15:7026-7032. [PMID: 31435632 DOI: 10.1039/c9sm00799g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We use moving light patterns to control the motion of Escherichia coli bacteria whose motility is photo-activated. Varying the pattern speed controls the magnitude and direction of the bacterial flux, and therefore the accumulation of cells in up- and down-stream reservoirs. We validate our results with two-dimensional simulations and a 1-dimensional analytic model, and use these to explore parameter space. We find that cell accumulation is controlled by a competition between directed flux and undirected, stochastic transport. Our results point to a number of design principles for using moving light patterns and light-activated micro-swimmers in a range of practical applications.
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Affiliation(s)
- Nick Koumakis
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
| | - Aidan T Brown
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
| | - Jochen Arlt
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
| | - Samuel E Griffiths
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
| | - Vincent A Martinez
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
| | - Wilson C K Poon
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK.
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105
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Chari SSN, Dasgupta C, Maiti PK. Scalar activity induced phase separation and liquid-solid transition in a Lennard-Jones system. SOFT MATTER 2019; 15:7275-7285. [PMID: 31490527 DOI: 10.1039/c9sm00962k] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report scalar activity induced phase separation and crystallization in a system of 3-d Lennard-Jones particles taken at state points spanning from the gas to the liquid regime using molecular dynamics simulation (MD). Scalar activity was introduced by increasing the temperature of half of the particles (labeled 'hot') while keeping the temperature of the other half constant at a lower value (labeled 'cold'). The relative temperature difference between the two subsystems is considered as a measure of the activity. From our simulations we observe that the two species tend to phase separate at sufficiently high activity ratio. The extent of separation is quantified by the defined order parameter and the entropy production during this process is determined by employing the two-phase thermodynamic (2PT) model and the standard modified Benedict-Webb-Rubin (MBWR) equation of state for a LJ fluid. We observe that the extent of the phase separation and entropy production increases with the density of the system. From a cluster analysis, we obtain the mean number of clusters ncl, and the mean size of the largest cluster n0 in the system, complementing each other. Bond orientation order parameters reveal that the so formed largest cluster also develops solid-like order consisting of both FCC and HCP packing. The presence of such crystalline order is also supported by a common neighbor analysis.
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Affiliation(s)
- S Siva Nasarayya Chari
- Department of Physics, Indian Institute of Science, C. V. Raman Ave, Bengaluru 560012, India.
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106
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Hoell C, Löwen H, Menzel AM. Multi-species dynamical density functional theory for microswimmers: Derivation, orientational ordering, trapping potentials, and shear cells. J Chem Phys 2019. [DOI: 10.1063/1.5099554] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Christian Hoell
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
| | - Andreas M. Menzel
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, D-40225 Düsseldorf, Germany
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107
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Foglino M, Locatelli E, Brackley CA, Michieletto D, Likos CN, Marenduzzo D. Non-equilibrium effects of molecular motors on polymers. SOFT MATTER 2019; 15:5995-6005. [PMID: 31292585 DOI: 10.1039/c9sm00273a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present a generic coarse-grained model to describe molecular motors acting on polymer substrates, mimicking, for example, RNA polymerase on DNA or kinesin on microtubules. The polymer is modeled as a connected chain of beads; motors are represented as freely diffusing beads which, upon encountering the substrate, bind to it through a short-ranged attractive potential. When bound, motors and polymer beads experience an equal and opposite active force, directed tangential to the polymer; this leads to motion of the motors along the polymer contour. The inclusion of explicit motors differentiates our model from other recent active polymer models. We study, by means of Langevin dynamics simulations, the effect of the motor activity on both the conformational and dynamical properties of the substrate. We find that activity leads, in addition to the expected enhancement of polymer diffusion, to an effective reduction of its persistence length. We discover that this effective "softening" is a consequence of the emergence of double-folded branches, or hairpins, and that it can be tuned by changing the number of motors or the force they generate. Finally, we investigate the effect of the motors on the probability of knot formation. Counter-intuitively our simulations reveal that, even though at equilibrium a more flexible substrate would show an increased knotting probability, motor activity leads to a marked decrease in the occurrence of knotted conformations with respect to equilibrium.
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Affiliation(s)
- M Foglino
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, UK
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108
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Lozano C, Liebchen B, Ten Hagen B, Bechinger C, Löwen H. Propagating density spikes in light-powered motility-ratchets. SOFT MATTER 2019; 15:5185-5192. [PMID: 31168529 DOI: 10.1039/c9sm00727j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Combining experiments and computer simulations, we use a spatially periodic and flashing light-field to direct the motion of phototactic active colloids. Here, the colloids self-organize into a density spike pattern, which resembles a shock wave and propagates over long distances, almost without dispersing. The underlying mechanism involves a synchronization of the colloids with the light-field, so that particles see the same intensity gradient each time the light-pattern is switched on, but no gradient in between (for example). This creates pulsating transport whose strength and direction can be controlled via the flashing protocol and the self-propulsion speed of the colloids. Our results might be useful for drug delivery applications and can be used to segregate active colloids by their speed.
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Affiliation(s)
- Celia Lozano
- Fachbereich Physik, Universität Konstanz, 78457 Konstanz, Germany
| | - Benno Liebchen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and Institut für Festkörperphysik, Technische Universität Darmstadt, 64289 Darmstadt, Germany.
| | - Borge Ten Hagen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany and Physics of Fluids Group and Max Planck Center Twente, Department of Science and Technology, MESA+ Institute, and J. M. Burgers Centre for Fluid Dynamics, University of Twente, 7500 AE Enschede, The Netherlands
| | | | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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109
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Chakraborti S, Pradhan P. Additivity and density fluctuations in Vicsek-like models of self-propelled particles. Phys Rev E 2019; 99:052604. [PMID: 31212568 DOI: 10.1103/physreve.99.052604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Indexed: 11/07/2022]
Abstract
We study coarse-grained density fluctuations in the disordered phase of the paradigmatic Vicsek-like models of self-propelled particles with alignment interactions and random self-propulsion velocities. By numerically integrating a fluctuation-response relation-the direct consequence of an additivity property-we compute logarithm of the large-deviation probabilities of the coarse-grained subsystem density, while the system is in the disordered fluid phase with vanishing macroscopic velocity. The large-deviation probabilities, computed within additivity, agree remarkably well with that obtained from direct microscopic simulations of the models. Our results provide evidence of the existence of an equilibriumlike chemical potential, which governs the coarse-grained density fluctuations in the Vicsek-like models. Moreover, comparison of the particle-number fluctuations among several self-propelled particle systems suggests a common mechanism through which the number fluctuations arise in such systems.
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Affiliation(s)
- Subhadip Chakraborti
- Department of Theoretical Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
| | - Punyabrata Pradhan
- Department of Theoretical Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India
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110
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Ai BQ, Li JJ, Li ZQ, Xiong JW, He YF. Rectification of chiral active particles driven by transversal temperature difference. J Chem Phys 2019; 150:184905. [PMID: 31091931 DOI: 10.1063/1.5096323] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Rectification of chiral active particles driven by transversal temperature difference is investigated in a two-dimensional periodic channel. Chiral active particles can be rectified by transversal temperature difference. Transport behaviors are qualitatively different for different wall boundary conditions. For the sliding boundary condition, the direction of transport completely depends on the chirality of particles. The average velocity is a peaked function of angular velocity or temperature difference. The average velocity increases linearly with the self-propulsion speed, while it decreases monotonically with the increase in the packing fraction. For randomized boundary condition, the transport behaviors become complex. When self-propulsion speed is small, in contrast with the sliding boundary condition, particles move in the opposite direction. However, for large self-propulsion speed, current reversals can occur by continuously changing the system parameters (angular velocity, temperature difference, packing fraction, and width of the channel).
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Affiliation(s)
- Bao-Quan Ai
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, China
| | - Jia-Jian Li
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, China
| | - Zhu-Qin Li
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, China
| | - Jian-Wen Xiong
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, China
| | - Ya-Feng He
- College of Physics Science and Technology, Hebei University, Baoding 071002, China
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111
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Lee M, Szuttor K, Holm C. A computational model for bacterial run-and-tumble motion. J Chem Phys 2019; 150:174111. [PMID: 31067902 DOI: 10.1063/1.5085836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this article we present a computational model for the simulation of self-propelled anisotropic bacteria. To this end we use a self-propelled particle model and augment it with a statistical algorithm for the run-and-tumble motion. We derive an equation for the distribution of reorientations of the bacteria that we use to analyze the statistics of the random walk and that allows us to tune the behavior of our model to the characteristics of an E. coli bacterium. We validate our implementation in terms of a single swimmer and demonstrate that our model is capable of reproducing E. coli's run-and-tumble motion with excellent accuracy.
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Affiliation(s)
- Miru Lee
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Kai Szuttor
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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112
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Epstein JM, Klymko K, Mandadapu KK. Statistical mechanics of transport processes in active fluids. II. Equations of hydrodynamics for active Brownian particles. J Chem Phys 2019; 150:164111. [DOI: 10.1063/1.5054912] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Jeffrey M. Epstein
- Department of Physics, University of California, Berkeley, California 94720, USA
| | - Katherine Klymko
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
| | - Kranthi K. Mandadapu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 USA
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113
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Kuron M, Stärk P, Burkard C, de Graaf J, Holm C. A lattice Boltzmann model for squirmers. J Chem Phys 2019; 150:144110. [PMID: 30981238 DOI: 10.1063/1.5085765] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The squirmer is a simple yet instructive model for microswimmers, which employs an effective slip velocity on the surface of a spherical swimmer to describe its self-propulsion. We solve the hydrodynamic flow problem with the lattice Boltzmann (LB) method, which is well-suited for time-dependent problems involving complex boundary conditions. Incorporating the squirmer into LB is relatively straightforward, but requires an unexpectedly fine grid resolution to capture the physical flow fields and behaviors accurately. We demonstrate this using four basic hydrodynamic tests: two for the far-field flow-accuracy of the hydrodynamic moments and squirmer-squirmer interactions-and two that require the near field to be accurately resolved-a squirmer confined to a tube and one scattering off a spherical obstacle-which LB is capable of doing down to the grid resolution. We find good agreement with (numerical) results obtained using other hydrodynamic solvers in the same geometries and identify a minimum required resolution to achieve this reproduction. We discuss our algorithm in the context of other hydrodynamic solvers and present an outlook on its application to multi-squirmer problems.
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Affiliation(s)
- Michael Kuron
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Philipp Stärk
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Christian Burkard
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Joost de Graaf
- Institute for Theoretical Physics, Center for Extreme Matter and Emergent Phenomena, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Christian Holm
- Institute for Computational Physics, University of Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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114
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Klamser JU, Kapfer SC, Krauth W. A kinetic-Monte Carlo perspective on active matter. J Chem Phys 2019; 150:144113. [DOI: 10.1063/1.5085828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Juliane U. Klamser
- Laboratoire de Physique Statistique, Département de physique de l’ENS, Ecole Normale Supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
| | - Sebastian C. Kapfer
- Theoretische Physik 1, FAU Erlangen-Nürnberg, Staudtstr. 7, 91058 Erlangen, Germany
| | - Werner Krauth
- Laboratoire de Physique Statistique, Département de physique de l’ENS, Ecole Normale Supérieure, PSL Research University, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Universités, UPMC Univ. Paris 06, CNRS, 75005 Paris, France
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115
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Szamel G. Mode-coupling theory for the steady-state dynamics of active Brownian particles. J Chem Phys 2019; 150:124901. [PMID: 30927902 DOI: 10.1063/1.5085752] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We present a theory for the steady-state dynamics of a two-dimensional system of spherically symmetric active Brownian particles. The derivation of the theory consists of two steps. First, we integrate out the self-propulsions and obtain a many-particle evolution equation for the probability distribution of the particles' positions. Second, we use the projection operator technique and a mode-coupling-like factorization approximation to derive an equation of motion for the density correlation function. The nonequilibrium character of the active system manifests itself through the presence of a steady-state correlation function that quantifies spatial correlations of microscopic steady-state currents of the particles. This function determines the dependence of the short-time dynamics on the activity. It also enters into the expression for the memory matrix and thus influences the long-time glassy dynamics.
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Affiliation(s)
- Grzegorz Szamel
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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116
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Jahanshahi S, Lozano C, Ten Hagen B, Bechinger C, Löwen H. Colloidal Brazil nut effect in microswimmer mixtures induced by motility contrast. J Chem Phys 2019; 150:114902. [PMID: 30901986 DOI: 10.1063/1.5083098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We numerically and experimentally study the segregation dynamics in a binary mixture of microswimmers which move on a two-dimensional substrate in a static periodic triangular-like light intensity field. The motility of the active particles is proportional to the imposed light intensity, and they possess a motility contrast, i.e., the prefactor depends on the species. In addition, the active particles also experience a torque aligning their motion towards the direction of the negative intensity gradient. We find a segregation of active particles near the intensity minima where typically one species is localized close to the minimum and the other one is centered around in an outer shell. For a very strong aligning torque, there is an exact mapping onto an equilibrium system in an effective external potential that is minimal at the intensity minima. This external potential is similar to (height-dependent) gravity such that one can define effective "heaviness" of the self-propelled particles. In analogy to shaken granular matter in gravity, we define a "colloidal Brazil nut effect" if the heavier particles are floating on top of the lighter ones. Using extensive Brownian dynamics simulations, we identify system parameters for the active colloidal Brazil nut effect to occur and explain it based on a generalized Archimedes' principle within the effective equilibrium model: heavy particles are levitated in a dense fluid of lighter particles if their effective mass density is lower than that of the surrounding fluid. We also perform real-space experiments on light-activated self-propelled colloidal mixtures which confirm the theoretical predictions.
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Affiliation(s)
- Soudeh Jahanshahi
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
| | - Celia Lozano
- Fachbereich Physik, Universität Konstanz, Konstanz D-78457, Germany
| | - Borge Ten Hagen
- Physics of Fluids Group and Max Planck Center Twente, Department of Science and Technology, MESA+ Institute, and J. M. Burgers Centre for Fluid Dynamics, University of Twente, 7500 AE Enschede, The Netherlands
| | | | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, D-40225 Düsseldorf, Germany
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117
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Caprini L, Marini Bettolo Marconi U. Active chiral particles under confinement: surface currents and bulk accumulation phenomena. SOFT MATTER 2019; 15:2627-2637. [PMID: 30810571 DOI: 10.1039/c8sm02492h] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this work, we study the stationary behavior of an assembly of independent chiral active particles under confinement by employing an extension of the active Ornstein-Uhlenbeck model. The chirality modeled by means of an effective torque term leads to a drastic reduction in the accumulation near the walls with respect to the case without handedness and to the appearance of currents parallel to the container walls accompanied by a large accumulation of particles in the inner region. In the case of two-dimensional chiral particles confined by harmonic walls, we determine the analytic form of the distribution of positions and velocities in two different situations: a rotationally invariant confining potential and an infinite channel with parabolic walls. Both these models display currents and chirality induced inner accumulation. These phenomena are further investigated by means of a more realistic description of a channel, where the wall and bulk regions are clearly separated. The corresponding current and density profiles are obtained by numerical simulations. At variance with the harmonic models, the third model shows a progressive emptying of the wall regions and the simultaneous enhancement of the bulk population. We explain such a phenomenon in terms of the combined effect of wall repulsive forces and chiral motion and provide a semiquantitative description of the current profile in terms of effective viscosity of the chiral gas.
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Affiliation(s)
- Lorenzo Caprini
- Gran Sasso Science Institute (GSSI), Via. F. Crispi 7, 67100 L'Aquila, Italy
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118
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Bacci M, Caflisch A, Vitalis A. On the removal of initial state bias from simulation data. J Chem Phys 2019; 150:104105. [PMID: 30876362 DOI: 10.1063/1.5063556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Classical atomistic simulations of biomolecules play an increasingly important role in molecular life science. The structure of current computing architectures favors methods that run multiple trajectories at once without requiring extensive communication between them. Many advanced sampling strategies in the field fit this mold. These approaches often rely on an adaptive logic and create ensembles of comparatively short trajectories whose starting points are not distributed according to the correct Boltzmann weights. This type of bias is notoriously difficult to remove, and Markov state models (MSMs) are one of the few strategies available for recovering the correct kinetics and thermodynamics from these ensembles of trajectories. In this contribution, we analyze the performance of MSMs in the thermodynamic reweighting task for a hierarchical set of systems. We show that MSMs can be rigorous tools to recover the correct equilibrium distribution for systems of sufficiently low dimensionality. This is conditional upon not tampering with local flux imbalances found in the data. For a real-world application, we find that a pure likelihood-based inference of the transition matrix produces the best results. The removal of the bias is incomplete, however, and for this system, all tested MSMs are outperformed by an alternative albeit less general approach rooted in the ideas of statistical resampling. We conclude by formulating some recommendations for how to address the reweighting issue in practice.
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Affiliation(s)
- Marco Bacci
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Vitalis
- University of Zurich, Department of Biochemistry, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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119
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Jakuszeit T, Croze OA, Bell S. Diffusion of active particles in a complex environment: Role of surface scattering. Phys Rev E 2019; 99:012610. [PMID: 30780271 DOI: 10.1103/physreve.99.012610] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Indexed: 11/07/2022]
Abstract
Experiments have shown that self-propelled particles can slide along the surface of a circular obstacle without becoming trapped over long times. Using simulations and theory, we study the impact of boundary conditions on the diffusive transport of active particles in an obstacle lattice. We find that particle dynamics with sliding boundary conditions result in large diffusivities even at high obstacle density, unlike classical specular reflection. These dynamics are very well described by a model based on run-and-tumble particles with microscopically derived reorientation functions arising from obstacle-induced tumbles. This model, however, fails to describe fine structure in the diffusivity at high obstacle density predicted by simulations for pusherlike collisions. Using a simple deterministic model, we show that this structure results from particles being guided by the lattice. Our results thus show how nonclassical surface scattering introduces a dependence on the lattice geometry at high densities. We discuss implications for the study of bacteria in complex environments.
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Affiliation(s)
- Theresa Jakuszeit
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Ottavio A Croze
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Samuel Bell
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
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120
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Krinninger P, Schmidt M. Power functional theory for active Brownian particles: General formulation and power sum rules. J Chem Phys 2019; 150:074112. [DOI: 10.1063/1.5061764] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Philip Krinninger
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - Matthias Schmidt
- Theoretische Physik II, Physikalisches Institut, Universität Bayreuth, D-95440 Bayreuth, Germany
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121
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Dev S, Chatterjee S. Run-and-tumble motion with steplike responses to a stochastic input. Phys Rev E 2019; 99:012402. [PMID: 30780313 DOI: 10.1103/physreve.99.012402] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 11/07/2022]
Abstract
We study a simple run-and-tumble random walk whose switching frequencies between run mode and tumble mode depend on a stochastic signal. We consider a particularly sharp, steplike dependence, where the run-to-tumble switching probability jumps from zero to one as the signal crosses a particular value (say y_{1}) from below. Similarly, tumble-to-run switching probability also shows a jump like this as the signal crosses another value (y_{2}<y_{1}) from above. We are interested in characterizing the effect of signaling noise on the long-time behavior of the random walker. We consider two different time-evolutions of the stochastic signal. In one case, the signal dynamics is an independent stochastic process and does not depend on the run-and-tumble motion. In this case we can analytically calculate the mean value and the complete distribution function of the run duration and tumble duration. In the second case, we assume that the signal dynamics is influenced by the spatial location of the random walker. For this system, we numerically measure the steady state position distribution of the random walker. We discuss some similarities and differences between our system and Escherichia coli chemotaxis, which is another well-known run-and-tumble motion encountered in nature.
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Affiliation(s)
- Subrata Dev
- Department of Theoretical Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
| | - Sakuntala Chatterjee
- Department of Theoretical Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700106, India
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122
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Shen Z, Würger A, Lintuvuori JS. Hydrodynamic self-assembly of active colloids: chiral spinners and dynamic crystals. SOFT MATTER 2019; 15:1508-1521. [PMID: 30672958 DOI: 10.1039/c8sm02352b] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Active colloids self-organise into a variety of collective states, ranging from highly motile "molecules" to complex 2D structures. Using large-scale simulations, we show that hydrodynamic interactions, together with a gravity-like aligning field, lead to tunable self-assembly of active colloidal spheres near a surface. The observed structures depend on the hydrodynamic characteristics: particles driven at the front, pullers, form small chiral spinners consisting of two or three particles, whereas those driven at the rear, pushers, assemble into large dynamic aggregates. The rotational motion of the puller spinners, arises from spontaneous breaking of the internal chirality. Our results show that the fluid flow mediates chiral transfer between neighbouring spinners. Finally we show that the chirality of the individual spinners controls the topology of the self-assembly in solution: homochiral samples assemble into a hexagonally symmetric 2D crystal lattice while racemic mixtures show reduced hexatic order with diffusion-like dynamics.
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Affiliation(s)
- Zaiyi Shen
- Univ. Bordeaux, CNRS, LOMA (UMR 5798), F-33405 Talence, France.
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123
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Nemoto T, Fodor É, Cates ME, Jack RL, Tailleur J. Optimizing active work: Dynamical phase transitions, collective motion, and jamming. Phys Rev E 2019; 99:022605. [PMID: 30934223 DOI: 10.1103/physreve.99.022605] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Indexed: 06/09/2023]
Abstract
Active work measures how far the local self-forcing of active particles translates into real motion. Using population Monte Carlo methods, we investigate large deviations in the active work for repulsive active Brownian disks. Minimizing the active work generically results in dynamical arrest; in contrast, despite the lack of aligning interactions, trajectories of high active work correspond to a collectively moving, aligned state. We use heuristic and analytic arguments to explain the origin of dynamical phase transitions separating the arrested, typical, and aligned regimes.
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Affiliation(s)
- Takahiro Nemoto
- Philippe Meyer Institute for Theoretical Physics, Physics Department, École Normale Supérieure & PSL Research University, 24 rue Lhomond, 75231 Paris Cedex 05, France
| | - Étienne Fodor
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Michael E Cates
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
| | - Robert L Jack
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, United Kingdom
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Julien Tailleur
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS/P7, Université Paris Diderot, 10 rue Alice Domon et Léonie Duquet, 75205 Paris cedex 13, France
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124
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Allen RJ, Waclaw B. Bacterial growth: a statistical physicist's guide. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2019; 82:016601. [PMID: 30270850 PMCID: PMC6330087 DOI: 10.1088/1361-6633/aae546] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Bacterial growth presents many beautiful phenomena that pose new theoretical challenges to statistical physicists, and are also amenable to laboratory experimentation. This review provides some of the essential biological background, discusses recent applications of statistical physics in this field, and highlights the potential for future research.
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Affiliation(s)
- Rosalind J Allen
- School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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125
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Kühn MJ, Schmidt FK, Farthing NE, Rossmann FM, Helm B, Wilson LG, Eckhardt B, Thormann KM. Spatial arrangement of several flagellins within bacterial flagella improves motility in different environments. Nat Commun 2018; 9:5369. [PMID: 30560868 PMCID: PMC6299084 DOI: 10.1038/s41467-018-07802-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 11/22/2018] [Indexed: 11/26/2022] Open
Abstract
Bacterial flagella are helical proteinaceous fibers, composed of the protein flagellin, that confer motility to many bacterial species. The genomes of about half of all flagellated species include more than one flagellin gene, for reasons mostly unknown. Here we show that two flagellins (FlaA and FlaB) are spatially arranged in the polar flagellum of Shewanella putrefaciens, with FlaA being more abundant close to the motor and FlaB in the remainder of the flagellar filament. Observations of swimming trajectories and numerical simulations demonstrate that this segmentation improves motility in a range of environmental conditions, compared to mutants with single-flagellin filaments. In particular, it facilitates screw-like motility, which enhances cellular spreading through obstructed environments. Similar mechanisms may apply to other bacterial species and may explain the maintenance of multiple flagellins to form the flagellar filament.
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Affiliation(s)
- Marco J Kühn
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, 35392, Gießen, Germany
| | - Felix K Schmidt
- Fachbereich Physik und LOEWE Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Nicola E Farthing
- Department of Physics, University of York, Heslington, York, YO10 5DD, UK
- Department of Mathematics, University of York, Heslington, York, YO10 5DD, UK
| | - Florian M Rossmann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, 35392, Gießen, Germany
| | - Bina Helm
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, 35392, Gießen, Germany
| | - Laurence G Wilson
- Department of Physics, University of York, Heslington, York, YO10 5DD, UK.
| | - Bruno Eckhardt
- Fachbereich Physik und LOEWE Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, 35032, Marburg, Germany.
| | - Kai M Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, 35392, Gießen, Germany.
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126
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Abstract
Active matter has been much studied for its intriguing properties such as collective motion, motility-induced phase separation and giant fluctuations. However, it has remained unclear how the states of active materials connect with the equilibrium phases. For two-dimensional systems, this is also because the understanding of the liquid, hexatic, and solid equilibrium phases and their phase transitions is recent. Here we show that two-dimensional self-propelled point particles with inverse-power-law repulsions moving with a kinetic Monte Carlo algorithm without alignment interactions preserve all equilibrium phases up to very large activities. Furthermore, at high activity within the liquid phase, a critical point opens up a gas–liquid motility-induced phase separation region. In our model, two-step melting and motility-induced phase separation are thus independent phenomena. We discuss the reasons for these findings to be common to a wide class of two-dimensional active systems. Adapting statistical physics tools to study active systems is challenging due to their non-equilibrium nature. Here the authors use simulations to present a phase diagram of a 2D active system, showing a two-step melting scenario far from equilibrium along with gas-liquid motility-induced phase separation.
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127
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Bianco V, Locatelli E, Malgaretti P. Globulelike Conformation and Enhanced Diffusion of Active Polymers. PHYSICAL REVIEW LETTERS 2018; 121:217802. [PMID: 30517801 DOI: 10.1103/physrevlett.121.217802] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Indexed: 06/09/2023]
Abstract
We study the dynamics and conformation of polymers composed by active monomers. By means of Brownian dynamics simulations we show that, when the direction of the self-propulsion of each monomer is aligned with the backbone, the polymer undergoes a coil-to-globulelike transition, highlighted by a marked change of the scaling exponent of the gyration radius. Concurrently, the diffusion coefficient of the center of mass of the polymer becomes essentially independent of the polymer size for sufficiently long polymers or large magnitudes of the self-propulsion. These effects are reduced when the self-propulsion of the monomers is not bound to be tangent to the backbone of the polymer. Our results, rationalized by a minimal stochastic model, open new routes for activity-controlled polymers and, possibly, for a new generation of polymer-based drug carriers.
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Affiliation(s)
- Valentino Bianco
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Wien 1090, Austria
- Faculty of Chemistry, Chemical Physics Deprtment, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, Madrid 28040, Spain
| | - Emanuele Locatelli
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Wien 1090, Austria
| | - Paolo Malgaretti
- Max Planck Institute for Intelligent Systems, Heisenbergstrasse 3, 70569 Stuttgart, Germany
- Institute for Theoretical Physics IV, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany
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128
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Caprini L, Marini Bettolo Marconi U. Active particles under confinement and effective force generation among surfaces. SOFT MATTER 2018; 14:9044-9054. [PMID: 30387799 DOI: 10.1039/c8sm01840e] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We consider the effect of geometric confinement on the steady-state properties of a one-dimensional active suspension subject to thermal noise. The random active force is modeled by an Ornstein-Uhlenbeck process and the system is studied both numerically, by integrating the Langevin governing equations, and analytically by solving the associated Fokker-Planck equation under suitable approximations. The comparison between the two approaches displays a fairly good agreement and in particular, we show that the Fokker-Planck approach can predict the structure of the system both in the wall region and in the bulk-like region where the surface forces are negligible. The simultaneous presence of thermal noise and active forces determines the formation of a layer, extending from the walls towards the bulk, where the system exhibits polar order. We relate the presence of such ordering to the mechanical pressure exerted on the container's walls and show how it depends on the separation of the boundaries and determines a Casimir-like attractive force mediated by the active suspension.
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Affiliation(s)
- Lorenzo Caprini
- Gran Sasso Science Institute (GSSI), Via. F. Crispi 7, 67100 L'Aquila, Italy
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129
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Zhu WJ, Zhong WR, Xiong JW, Ai BQ. Transport of particles driven by the traveling obstacle arrays. J Chem Phys 2018; 149:174906. [PMID: 30409003 DOI: 10.1063/1.5049719] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transport of three types of particles (passive particles, active particles without polar interaction, and active particles with polar interaction) is numerically investigated in the presence of traveling obstacle arrays. The transport behaviors are different for different types of particles. For passive particles, there exists an optimal traveling speed (or the translational diffusion) at which the average velocity of particles takes its maximum value. For active particles without polar interaction, the average velocity of particles is a peaked function of the obstacle traveling speed. The average velocity decreases monotonically with increase of the rotational diffusion for large driving speed, while it is a peaked function of the rotational diffusion for small driving speed. For active particles with polar interaction, interestingly, within particular parameter regimes, active particles can move in the opposite direction to the obstacles. The average velocity of particles can change its direction by changing the system parameters (the obstacles driving speed, the polar interaction strength, and the rotational diffusion).
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Affiliation(s)
- Wei-Jing Zhu
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, China
| | - Wei-Rong Zhong
- Siyuan Laboratory, Guangzhou Key Laboratory of Vacuum Coating Technologies and New Energy Materials, Department of Physics, Jinan University, Guangzhou 510632, China
| | - Jian-Wen Xiong
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, China
| | - Bao-Quan Ai
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, China
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130
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Petrelli I, Digregorio P, Cugliandolo LF, Gonnella G, Suma A. Active dumbbells: Dynamics and morphology in the coexisting region. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:128. [PMID: 30353425 DOI: 10.1140/epje/i2018-11739-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/05/2018] [Indexed: 06/08/2023]
Abstract
With the help of molecular dynamics simulations we study an ensemble of active dumbbells in purely repulsive interaction. We derive the phase diagram in the density-activity plane and we characterise the various phases with liquid, hexatic and solid character. The analysis of the structural and dynamical properties, such as enstrophy, mean-square displacement, polarisation, and correlation functions, shows the continuous character of liquid and hexatic phases in the coexisting region when the activity is increased starting from the passive limit.
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Affiliation(s)
- Isabella Petrelli
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, I-70126, Bari, Italy
| | - Pasquale Digregorio
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, I-70126, Bari, Italy
| | - Leticia F Cugliandolo
- Sorbonne Université, Laboratoire de Physique Théorique et Hautes Energies, CNRS UMR 7589, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Giuseppe Gonnella
- Dipartimento di Fisica, Università degli Studi di Bari and INFN, Sezione di Bari, via Amendola 173, I-70126, Bari, Italy
| | - Antonio Suma
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136, Trieste, Italy.
- Institute for Computational Molecular Science, College of Science and Technology, Temple University, 19122, Philadelphia, PA, USA.
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131
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Robertson B, Huang MJ, Chen JX, Kapral R. Synthetic Nanomotors: Working Together through Chemistry. Acc Chem Res 2018; 51:2355-2364. [PMID: 30207448 DOI: 10.1021/acs.accounts.8b00239] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Active matter, some of whose constituent elements are active agents that can move autonomously, behaves very differently from matter without such agents. The active agents can self-assemble into structures with a variety of forms and dynamical properties. Swarming, where groups of living agents move cooperatively, is commonly observed in the biological realm, but it is also seen in the physical realm in systems containing small synthetic motors. The existence of diverse forms of self-assembled structures has stimulated the search for new applications that involve active matter. We consider active systems where the agents are synthetic chemically powered motors with various shapes and sizes that operate by phoretic mechanisms, especially self-diffusiophoresis. These motors are able to move autonomously in solution by consuming fuel from their environment. Chemical reactions take place on catalytic portions of the motor surface and give rise to concentration gradients that lead to directed motion. They can operate in this way only if the chemical composition of the system is maintained in a nonequilibrium state since no net fluxes are possible in a system at equilibrium. In contrast to many other active systems, chemistry plays an essential part in determining the properties of the collective dynamics and self-assembly of these chemically powered motor systems. The inhomogeneous concentration fields that result from asymmetric motor reactions are felt by other motors in the system and strongly influence how they move. This chemical coupling effect often dominates other interactions due to fluid flow fields and direct interactions among motors and determines the form that the collective dynamics takes. Since we consider small motors with micrometer and nanometer sizes, thermal fluctuations are strong and cannot be neglected. The media in which the motors operate may not be simple and may contain crowding agents or molecular filaments that influence how the motors assemble and move. The collective motion is also influenced by the chemical gradients that arise from reactions in the surrounding medium. By adopting a microscopic perspective, where the motors, fluid environment, and crowding elements are treated at the coarse-grained molecular level, all of the many-body interactions that give rise to the collective behavior naturally emerge from the molecular dynamics. Through simulations and theory, this Account describes how active matter made from chemically powered nanomotors moving in simple and more complicated media can form different dynamical structures that are strongly influenced by interactions arising from cooperative chemical reactions on the motor surfaces.
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Affiliation(s)
- Bryan Robertson
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Mu-Jie Huang
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jiang-Xing Chen
- Department of Physics, Hangzhou Dianzi University, Hangzhou 310018, China
| | - Raymond Kapral
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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132
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Hoell C, Löwen H, Menzel AM. Particle-scale statistical theory for hydrodynamically induced polar ordering in microswimmer suspensions. J Chem Phys 2018; 149:144902. [DOI: 10.1063/1.5048304] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Christian Hoell
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Andreas M. Menzel
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
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133
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Liao JJ, Huang XQ, Ai BQ. Current reversals of active particles in time-oscillating potentials. SOFT MATTER 2018; 14:7850-7858. [PMID: 30209474 DOI: 10.1039/c8sm01291a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Rectification of interacting active particles is numerically investigated in a two-dimensional time-oscillating potential. It is found that the oscillation of the potential and the self-propulsion of active particles are two different types of nonequilibrium driving, which can induce net currents with opposite directions. For a given asymmetry of the potential, the direction of the transport is determined by the competition of the self-propulsion and the oscillation of the potential. There exists an optimal oscillating angular frequency (or self-propulsion speed) at which the average velocity takes its maximal positive or negative value. Remarkably, when the oscillation of the potential competes with the self-propulsion, the average velocity can change direction several times due to the change in the oscillating frequency. Especially, particles with different self-propulsion velocities will move in opposite directions and can be separated. Our results provide a novel and convenient method for controlling and manipulating the transport (or separation) of active particles.
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Affiliation(s)
- Jing-Jing Liao
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, China.
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134
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Shankar S, Marchetti MC. Hidden entropy production and work fluctuations in an ideal active gas. Phys Rev E 2018; 98:020604. [PMID: 30253539 DOI: 10.1103/physreve.98.020604] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Indexed: 11/07/2022]
Abstract
Collections of self-propelled particles that move persistently by continuously consuming free energy are a paradigmatic example of active matter. In these systems, unlike Brownian "hot colloids," the breakdown of detailed balance yields a continuous production of entropy at steady state, even for an ideal active gas. We quantify the irreversibility for a noninteracting active particle in two dimensions by treating both conjugated and time-reversed dynamics. By starting with underdamped dynamics, we identify a hidden rate of entropy production required to maintain persistence and prevent the rapidly relaxing momenta from thermalizing, even in the limit of very large friction. Additionally, comparing two popular models of self-propulsion with identical dissipation on average, we find that the fluctuations and large deviations in work done are markedly different, providing thermodynamic insight into the varying extents to which macroscopically similar active matter systems may depart from equilibrium.
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Affiliation(s)
- Suraj Shankar
- Physics Department and Syracuse Soft and Living Matter Program, Syracuse University, Syracuse, New York 13244, USA.,and Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
| | - M Cristina Marchetti
- Physics Department and Syracuse Soft and Living Matter Program, Syracuse University, Syracuse, New York 13244, USA.,and Kavli Institute for Theoretical Physics, University of California, Santa Barbara, California 93106, USA
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135
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Khadka U, Holubec V, Yang H, Cichos F. Active particles bound by information flows. Nat Commun 2018; 9:3864. [PMID: 30242284 PMCID: PMC6154969 DOI: 10.1038/s41467-018-06445-1] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 09/06/2018] [Indexed: 11/09/2022] Open
Abstract
Self-organization is the generation of order out of local interactions. It is deeply connected to many fields of science from physics, chemistry to biology, all based on physical interactions. The emergence of collective animal behavior is the result of self-organization processes as well, though they involve abstract interactions arising from sensory inputs, information processing, storage, and feedback. Resulting collective behaviors are found, for example, in crowds of people, flocks of birds, and swarms of bacteria. Here we introduce interactions between active microparticles which are based on the information about other particle positions. A real-time feedback of multiple active particle positions is the information source for the propulsion direction of these particles. The emerging structures require continuous information flows. They reveal frustrated geometries due to confinement to two dimensions and internal dynamical degrees of freedom that are reminiscent of physically bound systems, though they exist only as nonequilibrium structures.
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Affiliation(s)
- Utsab Khadka
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Viktor Holubec
- Institute for Theoretical Physics, Universität Leipzig, 04103, Leipzig, Germany.,Department of Macromolecular Physics, Faculty of Mathematics and Physics, Charles University, V Holešovičkách 2, CZ-180 00, Praha, Czech Republic
| | - Haw Yang
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Frank Cichos
- Peter Debye Institute for Soft Matter Physics, Universität Leipzig, 04103, Leipzig, Germany.
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136
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Wan KY, Goldstein RE. Time Irreversibility and Criticality in the Motility of a Flagellate Microorganism. PHYSICAL REVIEW LETTERS 2018; 121:058103. [PMID: 30118294 PMCID: PMC7616082 DOI: 10.1103/physrevlett.121.058103] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 03/27/2018] [Indexed: 06/08/2023]
Abstract
Active living organisms exhibit behavioral variability, partitioning between fast and slow dynamics. Such variability may be key to generating rapid responses in a heterogeneous, unpredictable environment wherein cellular activity effects continual exchanges of energy fluxes. We demonstrate a novel, noninvasive strategy for revealing nonequilibrium control of swimming-specifically, in an octoflagellate microalga. These organisms exhibit surprising features of flagellar excitability and mechanosensitivity, which characterize a novel, time-irreversible "run-stop-shock" motility comprising forward runs, knee-jerk shocks with dramatic beat reversal, and long stops during which cells are quiescent yet continue to exhibit submicron flagellar vibrations. Entropy production, associated with flux cycles arising in a reaction graph representation of the gait-switching dynamics, provides a direct measure of detailed balance violation in this primitive alga.
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Affiliation(s)
- Kirsty Y. Wan
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, United Kingdom
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Raymond E. Goldstein
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge CB3 0WA, United Kingdom
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137
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Koumakis N, Devailly C, Poon WCK. Motile bacteria in a critical fluid mixture. Phys Rev E 2018; 97:062604. [PMID: 30011513 DOI: 10.1103/physreve.97.062604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 11/07/2022]
Abstract
We studied the swimming of Escherichia coli bacteria in the vicinity of the critical point in a solution of the nonionic surfactant C_{12}E_{5} in buffer solution. In phase-contrast microscopy, each swimming cell produces a transient trail behind itself lasting several seconds. Comparing quantitative image analysis with simulations show that these trails are due to local phase reorganization triggered by differential adsorption. This contrasts with similar trails seen in bacteria swimming in liquid crystals, which are due to shear effects. We show how our trails are controlled, and use them to probe the structure and dynamics of critical fluctuations in the fluid medium.
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Affiliation(s)
- Nick Koumakis
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, United Kingdom
| | - Clémence Devailly
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, United Kingdom
| | - Wilson C K Poon
- SUPA and School of Physics & Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, United Kingdom
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138
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Pessot G, Löwen H, Menzel AM. Binary pusher–puller mixtures of active microswimmers and their collective behaviour. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1496291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Giorgio Pessot
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Andreas M. Menzel
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
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139
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Yoshinaga N, Liverpool TB. From hydrodynamic lubrication to many-body interactions in dense suspensions of active swimmers. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:76. [PMID: 29926216 DOI: 10.1140/epje/i2018-11683-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/25/2018] [Indexed: 06/08/2023]
Abstract
We study how hydrodynamic interactions affect the collective behaviour of active particles suspended in a fluid at high concentrations, with particular attention to lubrication forces which appear when the particles are very close to one another. We compute exactly the limiting behaviour of the hydrodynamic interactions between two spherical (circular) active swimmers in very close proximity to one another in the general setting in both three and (two) dimensions. Combining this with far-field interactions, we develop a novel numerical scheme which allows us to study the collective behaviour of large numbers of active particles with accurate hydrodynamic interactions when close to one another. We study active swimmers whose intrinsic flow fields are characterised by force dipoles and quadrupoles. Using this scheme, we are able to show that lubrication forces when the particles are very close to each other can play as important a role as long-range hydrodynamic interactions in determining their many-body behaviour. We find that when the swimmer force dipole is large, finite clusters and open gel-like clusters appear rather than complete phase separation. This suppression is due to near-field lubrication interactions. For swimmers with small force dipoles, we find surprisingly that a globally polar-ordered phase appears because near-field lubrication rather than long-range hydrodynamics dominates the alignment mechanism. Polar order is present for very large system sizes and is stable to fluctuations with a finite noise amplitude. We explain the emergence of polar order using a minimal model in which only the leading rotational effect of the near-field interaction is included. These phenomena are also reproduced in two dimensions.
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Affiliation(s)
- Natsuhiko Yoshinaga
- WPI - Advanced Institute for Materials Research, Tohoku University, 980-8577, Sendai, Japan.
- MathAM-OIL, AIST, 980-8577, Sendai, Japan.
- The Kavli Institute for Theoretical Physics, University of California, 93106, Santa Barbara, CA, USA.
| | - Tanniemola B Liverpool
- The Kavli Institute for Theoretical Physics, University of California, 93106, Santa Barbara, CA, USA
- School of Mathematics, University of Bristol, BS8 1TW, Bristol, UK
- BrisSynBio, Life Sciences Building, Tyndall Avenue, BS8 1TQ, Bristol, UK
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140
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Gnesotto FS, Mura F, Gladrow J, Broedersz CP. Broken detailed balance and non-equilibrium dynamics in living systems: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:066601. [PMID: 29504517 DOI: 10.1088/1361-6633/aab3ed] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Living systems operate far from thermodynamic equilibrium. Enzymatic activity can induce broken detailed balance at the molecular scale. This molecular scale breaking of detailed balance is crucial to achieve biological functions such as high-fidelity transcription and translation, sensing, adaptation, biochemical patterning, and force generation. While biological systems such as motor enzymes violate detailed balance at the molecular scale, it remains unclear how non-equilibrium dynamics manifests at the mesoscale in systems that are driven through the collective activity of many motors. Indeed, in several cellular systems the presence of non-equilibrium dynamics is not always evident at large scales. For example, in the cytoskeleton or in chromosomes one can observe stationary stochastic processes that appear at first glance thermally driven. This raises the question how non-equilibrium fluctuations can be discerned from thermal noise. We discuss approaches that have recently been developed to address this question, including methods based on measuring the extent to which the system violates the fluctuation-dissipation theorem. We also review applications of this approach to reconstituted cytoskeletal networks, the cytoplasm of living cells, and cell membranes. Furthermore, we discuss a more recent approach to detect actively driven dynamics, which is based on inferring broken detailed balance. This constitutes a non-invasive method that uses time-lapse microscopy data, and can be applied to a broad range of systems in cells and tissue. We discuss the ideas underlying this method and its application to several examples including flagella, primary cilia, and cytoskeletal networks. Finally, we briefly discuss recent developments in stochastic thermodynamics and non-equilibrium statistical mechanics, which offer new perspectives to understand the physics of living systems.
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Affiliation(s)
- F S Gnesotto
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, D-80333 München, Germany
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141
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Ai BQ, Shao ZG, Zhong WR. Mixing and demixing of binary mixtures of polar chiral active particles. SOFT MATTER 2018; 14:4388-4395. [PMID: 29770829 DOI: 10.1039/c8sm00444g] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We study a binary mixture of polar chiral (counterclockwise or clockwise) active particles in a two-dimensional box with periodic boundary conditions. Besides the excluded volume interactions between particles, the particles are also subjected to the polar velocity alignment. From the extensive Brownian dynamics simulations, it is found that the particle configuration (mixing or demixing) is determined by the competition between the chirality difference and the polar velocity alignment. When the chirality difference competes with the polar velocity alignment, the clockwise particles aggregate in one cluster and the counterclockwise particles aggregate in the other cluster; thus, the particles are demixed and can be separated. However, when the chirality difference or the polar velocity alignment is dominant, the particles are mixed. Our findings could be used for the experimental pursuit of the separation of binary mixtures of chiral active particles.
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Affiliation(s)
- Bao-Quan Ai
- Guangdong Provincial Key Laboratory of Quantum Engineering and Quantum Materials, School of Physics and Telecommunication Engineering, South China Normal University, Guangzhou 510006, China.
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142
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Nava LG, Großmann R, Peruani F. Markovian robots: Minimal navigation strategies for active particles. Phys Rev E 2018; 97:042604. [PMID: 29758683 DOI: 10.1103/physreve.97.042604] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Indexed: 01/08/2023]
Abstract
We explore minimal navigation strategies for active particles in complex, dynamical, external fields, introducing a class of autonomous, self-propelled particles which we call Markovian robots (MR). These machines are equipped with a navigation control system (NCS) that triggers random changes in the direction of self-propulsion of the robots. The internal state of the NCS is described by a Boolean variable that adopts two values. The temporal dynamics of this Boolean variable is dictated by a closed Markov chain-ensuring the absence of fixed points in the dynamics-with transition rates that may depend exclusively on the instantaneous, local value of the external field. Importantly, the NCS does not store past measurements of this value in continuous, internal variables. We show that despite the strong constraints, it is possible to conceive closed Markov chain motifs that lead to nontrivial motility behaviors of the MR in one, two, and three dimensions. By analytically reducing the complexity of the NCS dynamics, we obtain an effective description of the long-time motility behavior of the MR that allows us to identify the minimum requirements in the design of NCS motifs and transition rates to perform complex navigation tasks such as adaptive gradient following, detection of minima or maxima, or selection of a desired value in a dynamical, external field. We put these ideas in practice by assembling a robot that operates by the proposed minimalistic NCS to evaluate the robustness of MR, providing a proof of concept that is possible to navigate through complex information landscapes with such a simple NCS whose internal state can be stored in one bit. These ideas may prove useful for the engineering of miniaturized robots.
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Affiliation(s)
- Luis Gómez Nava
- Université Côte d'Azur, Laboratoire J. A. Dieudonné, UMR 7351 CNRS, Parc Valrose, F-06108 Nice Cedex 02, France
| | - Robert Großmann
- Université Côte d'Azur, Laboratoire J. A. Dieudonné, UMR 7351 CNRS, Parc Valrose, F-06108 Nice Cedex 02, France
| | - Fernando Peruani
- Université Côte d'Azur, Laboratoire J. A. Dieudonné, UMR 7351 CNRS, Parc Valrose, F-06108 Nice Cedex 02, France
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143
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Liang X, Lu N, Chang LC, Nguyen TH, Massoudieh A. Evaluation of bacterial run and tumble motility parameters through trajectory analysis. JOURNAL OF CONTAMINANT HYDROLOGY 2018; 211:26-38. [PMID: 29606374 DOI: 10.1016/j.jconhyd.2018.03.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 02/03/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
In this paper, a method for extraction of the behavior parameters of bacterial migration based on the run and tumble conceptual model is described. The methodology is applied to the microscopic images representing the motile movement of flagellated Azotobacter vinelandii. The bacterial cells are considered to change direction during both runs and tumbles as is evident from the movement trajectories. An unsupervised cluster analysis was performed to fractionate each bacterial trajectory into run and tumble segments, and then the distribution of parameters for each mode were extracted by fitting mathematical distributions best representing the data. A Gaussian copula was used to model the autocorrelation in swimming velocity. For both run and tumble modes, Gamma distribution was found to fit the marginal velocity best, and Logistic distribution was found to represent better the deviation angle than other distributions considered. For the transition rate distribution, log-logistic distribution and log-normal distribution, respectively, was found to do a better job than the traditionally agreed exponential distribution. A model was then developed to mimic the motility behavior of bacteria at the presence of flow. The model was applied to evaluate its ability to describe observed patterns of bacterial deposition on surfaces in a micro-model experiment with an approach velocity of 200 μm/s. It was found that the model can qualitatively reproduce the attachment results of the micro-model setting.
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Affiliation(s)
- Xiaomeng Liang
- Civil Engineering, The Catholic University of America, Washington, DC, USA
| | - Nanxi Lu
- Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Lin-Ching Chang
- Department of Computer Science, The Catholic University of America, Washington, DC, USA
| | - Thanh H Nguyen
- Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Arash Massoudieh
- Civil Engineering, The Catholic University of America, Washington, DC, USA.
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144
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Bhattacharyya D, Paul S, Ghosh S, Ray DS. Brownian dynamics of self-regulated particles with additional degrees of freedom: Symmetry breaking and homochirality. Phys Rev E 2018; 97:042125. [PMID: 29758662 DOI: 10.1103/physreve.97.042125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Indexed: 06/08/2023]
Abstract
We consider the Brownian motion of a collection of particles each with an additional degree of freedom. The degree of freedom of a particle (or, in general, a molecule) can assume distinct values corresponding to certain states or conformations. The time evolution of the additional degree of freedom of a particle is guided by those of its neighbors as well as the temperature of the system. We show that the local averaging over these degrees of freedom results in emergence of a collective order in the dynamics in the form of selection or dominance of one of the isomers leading to a symmetry-broken state. Our statistical model captures the basic features of homochirality, e.g., autocatalysis and chiral inhibition.
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Affiliation(s)
| | - Shibashis Paul
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Shyamolina Ghosh
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Deb Shankar Ray
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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145
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Paoluzzi M, Marconi UMB, Maggi C. Effective equilibrium picture in the xy model with exponentially correlated noise. Phys Rev E 2018; 97:022605. [PMID: 29548092 DOI: 10.1103/physreve.97.022605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Indexed: 11/07/2022]
Abstract
We study the effect of exponentially correlated noise on the xy model in the limit of small correlation time, discussing the order-disorder transition in the mean field and the topological transition in two dimensions. We map the steady states of the nonequilibrium dynamics into an effective equilibrium theory. In the mean field, the critical temperature increases with the noise correlation time τ, indicating that memory effects promote ordering. This finding is confirmed by numerical simulations. The topological transition temperature in two dimensions remains untouched. However, finite-size effects induce a crossover in the vortices proliferation that is confirmed by numerical simulations.
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Affiliation(s)
- Matteo Paoluzzi
- Department of Physics and Syracuse Soft & Living Matter Program, Syracuse University, Syracuse, New York 13244, USA
| | - Umberto Marini Bettolo Marconi
- Scuola di Scienze e Tecnologie, Università di Camerino, Via Madonna delle Carceri, 62032 Camerino, Italy.,INFN Perugia, 06123 Perugia, Italy
| | - Claudio Maggi
- NANOTEC-CNR, Institute of Nanotechnology, Soft and Living Matter Laboratory, Piazzale A. Moro 2, 00185 Rome, Italy
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146
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Arlt J, Martinez VA, Dawson A, Pilizota T, Poon WCK. Painting with light-powered bacteria. Nat Commun 2018; 9:768. [PMID: 29472614 PMCID: PMC5823856 DOI: 10.1038/s41467-018-03161-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/24/2018] [Indexed: 11/09/2022] Open
Abstract
Self-assembly is a promising route for micro- and nano-fabrication with potential to revolutionise many areas of technology, including personalised medicine. Here we demonstrate that external control of the swimming speed of microswimmers can be used to self assemble reconfigurable designer structures in situ. We implement such ‘smart templated active self assembly’ in a fluid environment by using spatially patterned light fields to control photon-powered strains of motile Escherichia coli bacteria. The physics and biology governing the sharpness and formation speed of patterns is investigated using a bespoke strain designed to respond quickly to changes in light intensity. Our protocol provides a distinct paradigm for self-assembly of structures on the 10 μm to mm scale. The ability to generate microscale patterns and control microswimmers may be useful for engineering smart materials. Here Arlt et al. use genetically modified bacteria with fast response to changes in light intensity to produce light-induced patterns.
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Affiliation(s)
- Jochen Arlt
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Vincent A Martinez
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Angela Dawson
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
| | - Teuta Pilizota
- School of Biological Sciences and Centre for Synthetic and Systems Biology, The University of Edinburgh, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Wilson C K Poon
- School of Physics and Astronomy, The University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK
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147
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Ginot F, Theurkauff I, Detcheverry F, Ybert C, Cottin-Bizonne C. Aggregation-fragmentation and individual dynamics of active clusters. Nat Commun 2018; 9:696. [PMID: 29449564 PMCID: PMC5814572 DOI: 10.1038/s41467-017-02625-7] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/15/2017] [Indexed: 12/24/2022] Open
Abstract
A remarkable feature of active matter is the propensity to self-organize. One striking instance of this ability to generate spatial structures is the cluster phase, where clusters broadly distributed in size constantly move and evolve through particle exchange, breaking or merging. Here we propose an exhaustive description of the cluster dynamics in apolar active matter. Exploiting large statistics gathered on thousands of Janus colloids, we measure the aggregation and fragmentation rates and rationalize the resulting cluster size distribution and fluctuations. We also show that the motion of individual clusters is entirely consistent with a model positing random orientation of colloids. Our findings establish a simple, generic model of cluster phase, and pave the way for a thorough understanding of clustering in active matter.
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Affiliation(s)
- F Ginot
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS,UMR 5306, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - I Theurkauff
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS,UMR 5306, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - F Detcheverry
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS,UMR 5306, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - C Ybert
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS,UMR 5306, Institut Lumière Matière, F-69622, Villeurbanne, France
| | - C Cottin-Bizonne
- Univ. Lyon, Université Claude Bernard Lyon 1, CNRS,UMR 5306, Institut Lumière Matière, F-69622, Villeurbanne, France.
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148
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Sartori P, Chiarello E, Jayaswal G, Pierno M, Mistura G, Brun P, Tiribocchi A, Orlandini E. Wall accumulation of bacteria with different motility patterns. Phys Rev E 2018; 97:022610. [PMID: 29548231 DOI: 10.1103/physreve.97.022610] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Indexed: 06/08/2023]
Abstract
We systematically investigate the role of different swimming patterns on the concentration distribution of bacterial suspensions confined between two flat walls, by considering wild-type motility Escherichia coli and Pseudomonas aeruginosa, which perform Run and Tumble and Run and Reverse patterns, respectively. The experiments count motile bacteria at different distances from the bottom wall. In agreement with previous studies, an accumulation of motile bacteria close to the walls is observed. Different wall separations, ranging from 100 to 250μm, are tested. The concentration profiles result to be independent on the motility pattern and on the walls' separation. These results are confirmed by numerical simulations, based on a collection of self-propelled dumbbells-like particles interacting only through steric interactions. The good agreement with the simulations suggests that the behavior of the investigated bacterial suspensions is determined mainly by steric collisions and self-propulsion, as well as hydrodynamic interactions.
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Affiliation(s)
- Paolo Sartori
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova, via Marzolo 8, 35131 Padova PD, Italy
| | - Enrico Chiarello
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova, via Marzolo 8, 35131 Padova PD, Italy
| | - Gaurav Jayaswal
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova, via Marzolo 8, 35131 Padova PD, Italy
| | - Matteo Pierno
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova, via Marzolo 8, 35131 Padova PD, Italy
| | - Giampaolo Mistura
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova, via Marzolo 8, 35131 Padova PD, Italy
| | - Paola Brun
- Dipartimento di Medicina Molecolare, Università di Padova, via Gabelli 63, 35121 Padova PD, Italy
| | - Adriano Tiribocchi
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova and INFN, via Marzolo 8, 35131 Padova PD, Italy
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia "Galileo Galilei," Università di Padova and INFN, via Marzolo 8, 35131 Padova PD, Italy
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149
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Marini Bettolo Marconi U, Sarracino A, Maggi C, Puglisi A. Self-propulsion against a moving membrane: Enhanced accumulation and drag force. Phys Rev E 2018; 96:032601. [PMID: 29347004 DOI: 10.1103/physreve.96.032601] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Indexed: 11/07/2022]
Abstract
Self-propulsion (SP) is a main feature of active particles (AP), such as bacteria or biological micromotors, distinguishing them from passive colloids. A renowned consequence of SP is accumulation at static interfaces, even in the absence of hydrodynamic interactions. Here we address the role of SP in the interaction between AP and a moving semipermeable membrane. In particular, we implement a model of noninteracting AP in a channel crossed by a partially penetrable wall, moving at a constant velocity c. With respect to both the cases of passive colloids with c>0 and AP with c=0, the AP with finite c show enhancement of accumulation in front of the obstacle and experience a largely increased drag force. This effect is understood in terms of an effective potential localised at the interface between particles and membrane, of height proportional to cτ/ξ, where τ is the AP's reorientation time and ξ the width characterizing the surface's smoothness (ξ→0 for hard core obstacles). An approximate analytical scheme is able to reproduce the observed density profiles and the measured drag force, in very good agreement with numerical simulations. The effects discussed here can be exploited for automatic selection and filtering of AP with desired parameters.
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Affiliation(s)
- U Marini Bettolo Marconi
- Scuola di Scienze e Tecnologie, Università di Camerino, Via Madonna delle Carceri, 62032, Camerino, INFN Perugia, Italy
| | - A Sarracino
- CNR-ISC and Dipartimento di Fisica, Sapienza Università di Roma, p.le A. Moro 2, 00185 Roma, Italy
| | - C Maggi
- CNR-NANOTEC and Dipartimento di Fisica, Sapienza Università di Roma, p.le A. Moro 2, 00185 Roma, Italy
| | - A Puglisi
- CNR-ISC and Dipartimento di Fisica, Sapienza Università di Roma, p.le A. Moro 2, 00185 Roma, Italy
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150
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Härtel A, Richard D, Speck T. Three-body correlations and conditional forces in suspensions of active hard disks. Phys Rev E 2018; 97:012606. [PMID: 29448434 DOI: 10.1103/physreve.97.012606] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Indexed: 06/08/2023]
Abstract
Self-propelled Brownian particles show rich out-of-equilibrium physics, for instance, the motility-induced phase separation (MIPS). While decades of studying the structure of liquids have established a deep understanding of passive systems, not much is known about correlations in active suspensions. In this work we derive an approximate analytic theory for three-body correlations and forces in systems of active Brownian disks starting from the many-body Smoluchowski equation. We use our theory to predict the conditional forces that act on a tagged particle and their dependence on the propulsion speed of self-propelled disks. We identify preferred directions of these forces in relation to the direction of propulsion and the positions of the surrounding particles. We further relate our theory to the effective swimming speed of the active disks, which is relevant for the physics of MIPS. To test and validate our theory, we additionally run particle-resolved computer simulations, for which we explicitly calculate the three-body forces. In this context, we discuss the modeling of active Brownian swimmers with nearly hard interaction potentials. We find very good agreement between our simulations and numerical solutions of our theory, especially for the nonequilibrium pair-distribution function. For our analytical results, we carefully discuss their range of validity in the context of the different levels of approximation we applied. This discussion allows us to study the individual contribution of particles to three-body forces and to the emerging structure. Thus, our work sheds light on the collective behavior, provides the basis for further studies of correlations in active suspensions, and makes a step towards an emerging liquid state theory.
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Affiliation(s)
- Andreas Härtel
- Institute of Physics, University of Freiburg, Hermann-Herder-Straße 3, 79104 Freiburg, Germany
| | - David Richard
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Thomas Speck
- Institute of Physics, Johannes Gutenberg-University Mainz, Staudinger Weg 9, 55128 Mainz, Germany
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